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wow-such-codewow-such-code
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petab model
1 parent 68a1e95 commit a3b0572

22 files changed

+687
-77
lines changed

‎pom.xml

+5
Original file line numberDiff line numberDiff line change
@@ -94,6 +94,11 @@
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<artifactId>picocli</artifactId>
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<version>4.6.2</version>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.dataformat</groupId>
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<artifactId>jackson-dataformat-yaml</artifactId>
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<version>2.17.2</version>
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</dependency>
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<dependency>
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<groupId>jline</groupId>
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<artifactId>jline</artifactId>

‎src/main/java/life/qbic/io/PetabParser.java

+175
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@@ -0,0 +1,175 @@
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package life.qbic.io;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
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import com.fasterxml.jackson.dataformat.yaml.YAMLMapper;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.FileReader;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Map;
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import java.util.Objects;
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import life.qbic.model.petab.MetaInformation;
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import life.qbic.model.petab.PetabMetadata;
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public class PetabParser {
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private final String META_INFO_YAML = "metaInformation.yaml";
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public PetabMetadata parse(String dataPath) {
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File directory = new File(dataPath);
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List<String> sourcePetabReferences = new ArrayList<>();
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File yaml = findYaml(directory);
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if (yaml != null) {
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BufferedReader reader = null;
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try {
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reader = new BufferedReader(new FileReader(yaml));
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while (true) {
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String line = reader.readLine();
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if (line == null) {
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break;
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}
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if (line.startsWith("openbisID")) {
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String datasetCode = line.strip().split(": ")[1];
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sourcePetabReferences.add(datasetCode);
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}
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}
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reader.close();
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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return new PetabMetadata(sourcePetabReferences);
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}
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private File findYaml(File directory) {
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for (File file : Objects.requireNonNull(directory.listFiles())) {
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if (file.isFile() && file.getName().equals(META_INFO_YAML)) {
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return file;
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}
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if (file.isDirectory()) {
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return findYaml(file);
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}
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}
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System.out.println(META_INFO_YAML + " not found");
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return null;
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}
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/**
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* adds key-value pairs to the bottom of a petab.yaml found below the provided path
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*
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* @param outputPath the path of the PEtab
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* @param properties map of properties to add
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*/
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public void addParameters(String outputPath, Map<String, String> properties) {
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File directory = new File(outputPath);
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File yaml = findYaml(directory);
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if (yaml != null) {
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FileOutputStream fos = null;
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try {
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fos = new FileOutputStream(yaml.getPath(), true);
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for (Map.Entry<String, String> entry : properties.entrySet()) {
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String line = entry.getKey() + ": " + entry.getValue() + "\n";
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fos.write(line.getBytes());
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}
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fos.close();
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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}
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public static void main(String[] args) throws IOException {
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File testfile = new File("/Users/afriedrich/git/openbis-20-scripts/example_petab/metaInformation.yaml");
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ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
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mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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MetaInformation metaInfo = mapper.readValue(testfile, MetaInformation.class);
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System.err.println(metaInfo);
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metaInfo.getUnits().setOpenbisParentIds(Arrays.asList("1","2"));
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metaInfo.getUnits().setOpenbisId("3");
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mapper.writeValue(new File("/Users/afriedrich/git/openbis-20-scripts/Output.yaml"), metaInfo);
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ObjectMapper mapper2 = new YAMLMapper();
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MetaInformation metaInfo2 = mapper2.readValue(testfile, MetaInformation.class);
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System.err.println(metaInfo2);
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/*
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MetaInformation{
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units=Units{
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measurement='some technique',
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time='min,
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t0 = timepoint of first intervention',
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stimulus='something',
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medium=Medium{type='DMEM', volume=1.5, unit='ml'},
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ncells=CellCountInfo{seeded=0.0, count='null', unit='null'},
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measurement_technique='immunublotting',
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openBISId='null', openBISParentIds=null,
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dateOfExperiment=[2024-04-30]
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},
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preprocessingInformation=null,
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measurementData=MeasurementData{
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measurement=Measurement{
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unit='intensity (a.u.)', lloq='null'},
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time=Time{unit='min'},
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replicateId=IdWithPattern{name='null', pattern='date_gel_replicate'}
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},
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experimentalCondition=ExperimentalCondition{conditionId=IdWithPattern{name='null', pattern='condition'},
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conditions=null}}
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ExperimentInformation:
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units:
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measurement: some technique
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time: min, t0 = timepoint of first intervention
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treatment:
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stimulus: something
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medium:
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type: DMEM
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volume: 1.5
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unit: ml
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ncells:
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seeded: 0.4
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ncellsCount: ~
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unit: mio
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measurement_technique: immunublotting
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openBISId: ~
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dateOfExperiment:
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- 2024-04-30
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PreprocessingInformation:
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normalizationStatus: Raw (data on linear scale)
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preprocessing:
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method: normalize by blotIt
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arguments:
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housekeeperObservableIds:
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description:
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measurementData:
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measurement:
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unit: intensity (a.u.)
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lloq: ~
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time:
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unit: min
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replicateId:
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pattern: date_gel_replicate
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experimentalCondition:
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conditionId:
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pattern: condition
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TGFb:
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unit: ng/ul
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GAS6:
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unit: ug/ml
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*/
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}
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}

‎src/main/java/life/qbic/io/commandline/DownloadDatasetCommand.java

-68
This file was deleted.

‎src/main/java/life/qbic/io/commandline/DownloadPetabCommand.java

+57
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,57 @@
1+
package life.qbic.io.commandline;
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3+
import ch.ethz.sis.openbis.generic.OpenBIS;
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import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
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import java.util.Collections;
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import java.util.List;
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import java.util.Optional;
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import life.qbic.App;
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import life.qbic.io.PetabParser;
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import life.qbic.model.DatasetWithProperties;
11+
import life.qbic.model.download.OpenbisConnector;
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import picocli.CommandLine.Command;
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import picocli.CommandLine.Mixin;
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import picocli.CommandLine.Parameters;
15+
16+
@Command(name = "download-petab",
17+
description = "Downloads PEtab dataset and stores some additional information from openbis in the petab.yaml")
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public class DownloadPetabCommand implements Runnable {
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20+
@Parameters(arity = "1", paramLabel = "dataset id", description = "The code of the dataset to download. Can be found via list-data.")
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private String datasetCode;
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@Parameters(arity = "1", paramLabel = "download path", description = "The local path where to store the downloaded data")
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private String outputPath;
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@Mixin
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AuthenticationOptions auth = new AuthenticationOptions();
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@Override
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public void run() {
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OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS(), auth.getDSS());
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OpenbisConnector openbis = new OpenbisConnector(authentication);
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32+
List<DataSet> datasets = openbis.findDataSets(Collections.singletonList(datasetCode));
33+
34+
if(datasets.isEmpty()) {
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System.out.println(datasetCode+" not found");
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return;
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}
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DatasetWithProperties result = new DatasetWithProperties(datasets.get(0));
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Optional<String> patientID = openbis.findPropertyInSampleHierarchy("PATIENT_DKFZ_ID",
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result.getExperiment().getIdentifier());
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patientID.ifPresent(s -> result.addProperty("patientID", s));
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result.addProperty("openbisID", datasetCode);
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44+
System.out.println("Found dataset, downloading.");
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System.out.println();
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openbis.downloadDataset(outputPath, datasetCode);
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System.out.println("Adding additional information to petab.yaml");
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System.out.println();
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PetabParser parser = new PetabParser();
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parser.addParameters(outputPath, result.getProperties());
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System.out.println("Done");
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}
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}

‎src/main/java/life/qbic/io/commandline/UploadDatasetCommand.java

-5
Original file line numberDiff line numberDiff line change
@@ -70,9 +70,4 @@ private boolean pathValid(String dataPath) {
7070
return new File(dataPath).exists();
7171
}
7272

73-
private String getTimeStamp() {
74-
final String PATTERN_FORMAT = "YYYY-MM-dd_HHmmss";
75-
DateTimeFormatter formatter = DateTimeFormatter.ofPattern(PATTERN_FORMAT);
76-
return LocalDateTime.ofInstant(Instant.now(), ZoneOffset.UTC).format(formatter);
77-
}
7873
}

‎src/main/java/life/qbic/io/commandline/UploadPetabResultCommand.java

+72
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@@ -0,0 +1,72 @@
1+
package life.qbic.io.commandline;
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import ch.ethz.sis.openbis.generic.OpenBIS;
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import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
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import java.io.File;
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import java.nio.file.Path;
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import java.util.ArrayList;
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import java.util.List;
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import life.qbic.App;
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import life.qbic.io.PetabParser;
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import life.qbic.model.download.OpenbisConnector;
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import picocli.CommandLine.Command;
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import picocli.CommandLine.Mixin;
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import picocli.CommandLine.Option;
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import picocli.CommandLine.Parameters;
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@Command(name = "upload-petab-result",
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description = "uploads a petab based on other PETab downloaded from openbis and attaches it to a provided experiment and any datasets referenced in the PETab metadata.")
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public class UploadPetabResultCommand implements Runnable {
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@Parameters(arity = "1", paramLabel = "file/folder", description = "The path to the file or folder to upload")
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private String dataPath;
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@Parameters(arity = "1", paramLabel = "experiment ID", description = "The full identifier of the experiment the data should be attached to. "
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+ "The identifier must be of the format: /space/project/experiment")
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private String experimentID;
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@Option(arity = "1..*", paramLabel = "<parent_datasets>", description = "Optional list of dataset codes to act"
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+ " as parents for the upload. E.g. when this dataset has been generated using these datasets as input.", names = {"-pa", "--parents"})
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private List<String> parents = new ArrayList<>();
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@Mixin
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AuthenticationOptions auth = new AuthenticationOptions();
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private OpenbisConnector openbis;
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private PetabParser petabParser = new PetabParser();
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@Override
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public void run() {
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OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS(), auth.getDSS());
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openbis = new OpenbisConnector(authentication);
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if(!pathValid(dataPath)) {
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System.out.printf("Path %s could not be found%n", dataPath);
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return;
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}
44+
if(!experimentExists(experimentID)) {
45+
System.out.printf("Experiment %s could not be found%n", experimentID);
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return;
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}
48+
parents = petabParser.parse(dataPath).getSourcePetabReferences();
49+
if(!datasetsExist(parents)) {
50+
System.out.printf("One or more datasets %s could not be found%n", parents);
51+
return;
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}
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System.out.println();
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System.out.println("Parameters verified, uploading dataset...");
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System.out.println();//TODO copy and remove source references
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DataSetPermId result = openbis.registerDataset(Path.of(dataPath), experimentID, parents);
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System.out.printf("Dataset %s was successfully created%n", result.getPermId());
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}
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private boolean datasetsExist(List<String> datasetCodes) {
61+
return openbis.findDataSets(datasetCodes).size() == datasetCodes.size();
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}
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private boolean experimentExists(String experimentID) {
65+
return openbis.experimentExists(experimentID);
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}
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private boolean pathValid(String dataPath) {
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return new File(dataPath).exists();
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}
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}

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